Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice

This paper describes a fluorescence in situ hybridization (FISH) analysis o f three different repetitive sequence families, which were mapped to mitoti c metaphase chromosomes and extended DNA fibers (EDFs) of the two subspecie s of rice (Oryza sativa), indica and japonica (2n = 2x = 24). The repeat fa milies studied were(1) the tandem repeat sequence A (TrsA), a functionally non-significant repeat, (2) the [TTTA-GCG], telomere sequencer a non-transc ribed, tandemly repeated but functionally significant repeat: and (3) the S S ribosomal RNA (5S rDNA). FISH of the TrsA repeat to metaphase chromosomes of indica and japonica cultivars revealed clear signals at the distal ends of twelve and four chromosomes, respectively. As shown ill a previous repo rt, the 17S ribosomal RNA genes (17S rDNA) are located at the nucleolus org anizers (NORs) on chromosomes 9 and 10 of the indica cultivar. However, the japonica rice lacked the rDNA signals on chromosome 10. The size of the 5S rDNA repeat block, which was mapped on the chromosome 11 of both cultivars , was 1.22 times larger in the indica than in the japonica genome. The telo meric repeat arrays at the distal ends of all chromosome arms were on avera ge three times longer in the indica genome than in the japonica genome. Flo w cytometric measurements revealed that the nuclear DNA content of indica r ice is 9.7% higher than that of japonica rice. Our data suggest that differ ent repetitive sequence families contribute significantly to the variation in genome size between indica and japonica rice, though to different extent s. The increase or decrease in the copy number of several repetitive sequen ces examined here may indicate the existence of a directed change in genome size in rice. Possible reasons for this phenomenon of concurrent evolution of various repeat families are discussed.